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Protocols

PhenoSeq specifications

Information


Unique identifier OMICS_12142
Name PhenoSeq
Interface Web user interface
Restrictions to use None
Input data Unaligned sequence(s) containing the V3 region
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens
  • Viruses
    • Human immunodeficiency virus 1
    • Human immunodeficiency virus 2

Maintainer


  • person_outline Paul Gorry

Publication for PhenoSeq

PhenoSeq citations

 (12)
library_books

Phenotypic co receptor tropism and Maraviroc sensitivity in HIV 1 subtype C from East Africa

2018
Sci Rep
PMCID: 5799384
PMID: 29403064
DOI: 10.1038/s41598-018-20814-2

[…] However, all the machine-learning GTT tools have been developed primarily for HIV-1B and are now applied also with newly available V3-sequences of non-B subtype HIV-1. More recently a GTT tool called PhenoSeq was developed, which claims to be reliably predictive for the tropism of HIV-1 subtypes A, B, C, D, 01_AE and 02_AG.Several guidelines have recommended pre-therapy GTT for patients initiating […]

library_books

Prediction of coreceptor usage by five bioinformatics tools in a large Ethiopian HIV 1 subtype C cohort

2017
PLoS One
PMCID: 5571954
PMID: 28841646
DOI: 10.1371/journal.pone.0182384

[…] rom a large cohort of HIV-1C infected Ethiopians and compared the predicted tropism with clinical data and ART outcomes.The bioinformatics methods have been developed largely on HIV-1B data, although PhenoSeq-C [] and C-PSSM [] have been trained on HIV-1C. In our study, each bioinformatics tool predicted a similar prevalence of R5 viruses in the HIV-1C infected Ethiopians. This is in concordance w […]

call_split

HIV 1 and SIV Predominantly Use CCR5 Expressed on a Precursor Population to Establish Infection in T Follicular Helper Cells

2017
Front Immunol
PMCID: 5399036
PMID: 28484447
DOI: 10.3389/fimmu.2017.00376
call_split See protocol

[…] mize sample size, as these proviruses were functional at the time of entry. HIV-1 coreceptor usage was predicted using Geno2Pheno[coreceptor] (G2P) (), Web PSSM (both x4r5 and sinsi matrices) (), and PhenoSeq-B (). […]

library_books

Partial HIV C2V3 envelope sequence analysis reveals association of coreceptor tropism, envelope glycosylation and viral genotypic variability among Kenyan patients on HAART

2017
Virol J
PMCID: 5310022
PMID: 28196510
DOI: 10.1186/s12985-017-0703-y

[…] /coreceptor.geno2pheno.org/index.php) under the section that allows for examination of co-receptor usage. Similarly, the sequences were applied to WebPSSM [], Raymond rule [], Esbjörnsson rule [] and Phenoseq []. For Geno2Pheno, we first applied a false positive rate (FPR) cut-off of 10% (FPR10), being the standard recommendation of the ‘European Consensus Group on clinical management of HIV-1 tro […]

library_books

Monophylogenetic HIV 1C epidemic in Ethiopia is dominated by CCR5 tropic viruses–an analysis of a prospective country wide cohort

2017
BMC Infect Dis
PMCID: 5219668
PMID: 28061826
DOI: 10.1186/s12879-016-2163-1

[…] either positions 11 and 25 of the V3 loop are positively charged []. More sophisticated models have been developed that outperform the 11/25 rule, e.g. position specific scoring matrix (PSSM) [] and PhenoSeq []. The most widely used geno2pheno and PSSM tools are highly concordant (>85%) []. In our study the geno2pheno tools were chosen as the European Guidelines recommend its use []. Moreover, si […]

library_books

Sequential CCR5 Tropic HIV 1 Reactivation from Distinct Cellular Reservoirs following Perturbation of Elite Control

2016
PLoS One
PMCID: 4942039
PMID: 27403738
DOI: 10.1371/journal.pone.0158854

[…] substitution model, estimating all parameters independently for each branch. The four tests were performed within HyPhy []. To predict viral tropism we used two genotypic algorithms Geno2pheno [] and Phenoseq [, ]. Concurrence between both programs was required in order to assign CXCR4 tropism to a particular env sequence. […]

Citations

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PhenoSeq institution(s)
Center for Virology, Burnet Institute, Melbourne, Australia

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